”Mulla on koko ajan enempi ja enempi semmonen kuva, et me ymmärretään edelleen paljon se turvallinen koulu väärin”:tapaustutkimus erään etelä-suomalaisen erityiskoulun henkilökunnan näkemyksistä turvallisen pedagogiikan työkalusta

Tiivistelmä. Tämän pro gradu -tutkielman tavoitteena on selvittää erään Etelä-Suomessa sijaitsevan erityiskoulun henkilökunnan käsityksiä turvallisen pedagogiikan työkalusta ja sen käytöstä heidän työssään. Turvallisen pedagogiikan työkalu on Kankaan koulun kehittämä pedagogisen toiminnan malli, jonka tavoitteena on tukea ja ohjata yksilön ja koko kouluyhteisön tasolla pedagogista toimintaa niin, että oppimisympäristöistä tulee oppilaiden turvallisuuden tunnetta, hyvinvointia ja oppimista tukevia. Suomalainen oppilaitoksen ja oppilaiden turvallisuuden tunteen tutkimus on keskittynyt lähinnä oppimisympäristöjen fyysisen, psyykkisen ja sosiaalisen turvallisuuden tarkasteluun. Turvallisuuden ja hyvinvoinnin käsitteet ovat hyvin laajoja ja moniulotteisia. Tässä tutkimuksessa keskitytään kuitenkin yksilön subjektiiviseen kokemukseen turvallisuudesta ja hyvinvoinnista ja miten niitä voidaan pedagogisella toiminnalla edistää oppilaitoksissa. Pedagoginen toiminta on kasvatuksellista toimintaa, joka pohjautuu yksilön aiempiin uskomuksiin, tietoon ja kokemuksiin. Turvallisen pedagogiikan työkalun mukaisessa pedagogisessa toiminnassa oppilaiden turvallisuutta ja hyvinvointia pyritään tukemaan motivointikeinojen, ohjeistuksen ja rytmin, ennakoinnin, huoltajien ja koulun välisen luottamuksen, toiston, rakenteiden sekä aikuisten roolien ja yhteisöllisyyden keinoin. Tutkimuksen tarkoituksena on perehtyä koulun henkilökunnan näkemyksiin siitä, miten he hyödyntävät turvallisen pedagogiikan työkalua omassa työssään sekä sitä, minkälaisia näkemyksiä heillä on turvallisen pedagogiikan työkalun sisällöistä sekä niiden merkityksestä heidän työssään. Tämä tutkimus toteutettiin laadullisena tapaustutkimuksena, jossa on hyödynnetty fenomenografista tutkimusotetta. Aineisto kerättiin teemahaastatteluiden avulla. Haastatteluiden pohjalta voitiin todeta, että turvallisen pedagogiikan työkalua hyödynnettiin osana yksilön pedagogista toimintaa, osana koulun toimintakulttuurin ja toiminnan kehittämisen työkaluna. Turvallisen pedagogiikan työkalujen sisältöjä ja sen hyödyntämistä pidettiin ammattitaidon perustana, ammatillisen toiminnan ja toimintakulttuurin tukena sekä oppilaan laaja-alaisena tukena. Koulun henkilökunnan pedagogisen toiminnan tarkastelu oppilaiden turvallisuuden tunteen ja hyvinvoinnin edistämisessä on jäänyt vähäiselle huomiolle suomalaisissa tutkimuksissa, vaikka sitä olisi olennaista tarkastella koulukontekstissa. Olisikin tarpeellista, että myös pedagogiseen turvallisuuteen kiinnitetään jatkossa huomiota, jotta oppilaisen turvallisuuden tunnetta ja hyvinvointia voidaan tukea kaikilla turvallisuuden osa-alueilla koululaitoksissa

Alignment of gene expression profiles from test samples against a reference database: New method for context-specific interpretation of microarray data

Alignment of gene expression profiles from test samples against a reference database: New method for context-specific interpretation of microarray data Kilpinen, Sami K Ojala, Kalle A Kallioniemi, Olli P England BioData mining BioData Min. 2011 Mar 31;4:5. engBACKGROUND: Gene expression microarray data have been organized and made available as public databases, but the utilization of such highly heterogeneous reference datasets in the interpretation of data from individual test samples is not as developed as e.g. in the field of nucleotide sequence comparisons. We have created a rapid and powerful approach for the alignment of microarray gene expression profiles (AGEP) from test samples with those contained in a large annotated public reference database and demonstrate here how this can facilitate interpretation of microarray data from individual samples. METHODS: AGEP is based on the calculation of kernel density distributions for the levels of expression of each gene in each reference tissue type and provides a quantitation of the similarity between the test sample and the reference tissue types as well as the identity of the typical and atypical genes in each comparison. As a reference database, we used 1654 samples from 44 normal tissues (extracted from the Genesapiens database). RESULTS: Using leave-one-out validation, AGEP correctly defined the tissue of origin for 1521 (93.6%) of all the 1654 samples in the original database. Independent validation of 195 external normal tissue samples resulted in 87% accuracy for the exact tissue type and 97% accuracy with related tissue types. AGEP analysis of 10 Duchenne muscular dystrophy (DMD) samples provided quantitative description of the key pathogenetic events, such as the extent of inflammation, in individual samples and pinpointed tissue-specific genes whose expression changed (SAMD4A) in DMD. AGEP analysis of microarray data from adipocytic differentiation of mesenchymal stem cells and from normal myeloid cell types and leukemias provided quantitative characterization of the transcriptomic changes during normal and abnormal cell differentiation. CONCLUSIONS: The AGEP method is a widely applicable method for the rapid comprehensive interpretation of microarray data, as proven here by the definition of tissue- and disease-specific changes in gene expression as well as during cellular differentiation. The capability to quantitatively compare data from individual samples against a large-scale annotated reference database represents a widely applicable paradigm for the analysis of all types of high-throughput data. AGEP enables systematic and quantitative comparison of gene expression data from test samples against a comprehensive collection of different cell/tissue types previously studied by the entire research community.Peer reviewe

Non-tuberculous Mycobacteria can Cause Disseminated Mycobacteriosis in Cats

Mycobacteriosis caused by non-tuberculous mycobacteria (NTM) is a rising concern in human medicine both in immunocompromised and immunocompetent patients. In cats, mycobacteriosis caused by NTM is considered mostly to be a focal or dermal infection, with disseminated disease mostly caused by Mycobacterium avium. We describe three cases of disseminated mycobacteriosis in cats, caused by Mycobacterium malmoense, Mycobacterium branderi/shimoidei and M. avium, with no identified underlying immunosuppression. In all cases, extracellular mycobacteria were seen in the pulmonary epithelium, intestinal lumen and glomerular tufts, which could affect the shedding of the organism. The present study highlights the importance of mycobacteriosis as a differential even in immunocompetent animals. Considering the close relationship of owners and pets and the potential presence of free mycobacteria in secretions, cats should be considered as a possible environmental reservoir for mycobacteria. (C) 2018 Elsevier Ltd. All rights reserved.Peer reviewe

Correlation of intestinal histopathologic findings with mucosa-attached bacteria, clinical disease activity, and clinical outcome in dogs with chronic enteropathies

Peer reviewe

S100A12 concentrations and myeloperoxidase activity in the intestinal mucosa of healthy dogs

Background: Relatively few laboratory markers have been evaluated for the detection or monitoring of intestinal inflammation in canine chronic enteropathies, including inflammatory bowel disease (IBD). Previous research found that the intestinal mucosal levels of S100A12 and myeloperoxidase (MPO), as biomarkers of gut inflammation, were elevated in human patients with IBD. To date, the S100A12 and MPO levels in intestinal mucosal samples from either healthy dogs or from dogs suffering from IBD remain unreported. Therefore, this study aimed to evaluate the mucosal S100A12 and MPO levels in four different parts of the intestine (duodenum, jejunum, ileum and colon) in 12 healthy laboratory Beagle dogs using the ELISA and spectrophotometric methods, respectively. Results: Based on histological examinations, the recorded findings for all the samples were considered normal. The mucosal concentration of S100A12 in the ileum was significantly higher than in all other segments of the intestine (p <0.05). MPO activity was significantly higher in the ileal, jejunal and duodenal than in colonic mucosal samples (p <0.05). Moreover, its concentration was higher in the jejunum than in the duodenum. Conclusions: This study showed that S100A12 and MPO are reliably detectable in canine intestinal mucosa. The assays used appeared to be sufficient to further evaluate the role of S100A12 and MPO in the pathogenesis of canine chronic enteropathies, including IBD. These biomarkers may play a role in the initial detection of gut inflammation suggesting the need for further investigations to confirm IBD or to differentiate between IBD subtypes. Understanding the role of S100A12 and MPO in the pathogenesis of chronic intestinal inflammation in future may result in an improved understanding of canine chronic intestinal inflammation.Peer reviewe

S100A12 concentrations and myeloperoxidase activities are increased in the intestinal mucosa of dogs with chronic enteropathies

Background: Intestinal mucosal S100A12 and myeloperoxidase (MPO) are inflammatory biomarkers in humans with inflammatory bowel disease (IBD). However, these biomarkers have not been studied in the intestinal mucosa of dogs with chronic enteropathies (CE), even though dogs with CE have increased S100A12 concentrations in feces and serum. This study investigated mucosal S100A12 concentrations and MPO activities in both dogs with CE and healthy Beagles. ELISA (S100A12 concentrations) and spectrophotometric methods (MPO activity) were used. The associations of both biomarkers with canine IBD activity index (CIBDAI), histopathologic findings, clinical outcome, and serum albumin concentrations were also investigated. We studied intestinal mucosal samples originating from different intestinal regions of 40 dogs with CE and 18 healthy Beagle dogs (duodenum, ileum, colon, and cecum). Results: Compared with healthy Beagles, mucosal S100A12 concentrations in dogs with CE were significantly higher in the duodenum (p <0.0001) and colon (p = 0.0011), but not in the ileum (p = 0.2725) and cecum (p = 0. 2194). Mucosal MPO activity of dogs with CE was significantly higher in the duodenum (p <0.0001), ileum (p = 0. 0083), colon (p <0.0001), and cecum (p = 0.0474). Mucosal S100A12 concentrations in the duodenum were significantly higher if the inflammatory infiltrate consisted mainly of neutrophils (p = 0.0439) or macrophages (p = 0.037). Mucosal S100A12 concentrations also showed a significant association with the severity of total histopathological injury and epithelial injury in the colon (p <0.05). Mucosal MPO activity showed a significant association (p <0.05) with the severity of total histopathological injury, epithelial injury, and eosinophil infiltration in the duodenum. There was no significant association of both biomarkers with CIBDAI or clinical outcome. Conclusions: This study showed that both mucosal S100A12 concentrations and MPO activities are significantly increased in the duodenum and colon of dogs with CE; mucosal MPO was also increased in the ileum and cecum. Future research should focus on assessing the clinical utility of S100A12 and MPO as diagnostic markers in dogs with CE.Peer reviewe

Bacterial Biogeography of the Colon in Dogs With Chronic Inflammatory Enteropathy

The intestinal microbiota is believed to play a role in the pathogenesis of inflammatory bowel disease in humans and chronic inflammatory enteropathy (CIE) in dogs. While most previous studies have described the gut microbiota using sequencing methods, it is fundamental to assess the spatial distribution of the bacteria for a better understanding of their relationship with the host. The microbiota in the colonic mucosa of 22 dogs with CIE and 11 control dogs was investigated using fluorescence in situ hybridization (FISH) with a universal eubacterial probe (EUB338) and specific probes for select bacterial groups. The number of total bacteria labeled with EUB338 probe was lower within the colonic crypts of dogs with CIE compared to controls. Helicobacter spp. and Akkermansia spp. were decreased on the colonic surface and in the crypts of dogs with CIE. Dogs with CIE had increased number of Escherichia coli/Shigella spp. on the colonic surface and within the crypts compared to control dogs. In conclusion, the bacterial microbiota in the colonic mucosa differed between dogs with and without CIE, with depletion of the crypt bacteria in dogs with CIE. The crypt bacterial species that was intimately associated with the host mucosa in control dogs was composed mainly of Helicobacter spp.Peer reviewe

Differentiation of human induced pluripotent stem cells into cortical neural stem cells

Efficient and effective methods for converting human induced pluripotent stem cells into differentiated derivatives are critical for performing robust, large-scale studies of development and disease modelling, and for providing a source of cells for regenerative medicine. Here, we describe a 14-day neural differentiation protocol which allows for the scalable, simultaneous differentiation of multiple iPSC lines into cortical neural stem cells We currently employ this protocol to differentiate and compare sets of engineered iPSC lines carrying loss of function alleles in developmental disorder associated genes, alongside isogenic wildtype controls. Using RNA sequencing (RNA-Seq), we can examine the changes in gene expression brought about by each disease gene knockout, to determine its impact on neural development and explore mechanisms of disease. The 10-day Neural Induction period uses the well established dual-SMAD inhibition approach combined with Wnt/beta-Catenin inhibition to selectively induce formation of cortical NSCs. This is followed by a 4-day Neural Maintenance period facilitating NSC expansion and rosette formation, and NSC cryopreservation. We also describe methods for thawing and passaging the cryopreserved NSCs, which are useful in confirming their viability for further culture. Routine implementation of immunocytochemistry Quality Control confirms the presence of PAX6-positive and/or FOXG1-positive NSCs and the absence of OCT4-positive iPSCs after differentiation. RNA-Seq, flow cytometry, immunocytochemistry (ICC) and RT-qPCR provide additional confirmation of robust presence of NSC markers in the differentiated cells. The broader utility and application of our protocol is demonstrated by the successful differentiation of wildtype iPSC lines from five additional independent donors. This paper thereby describes an efficient method for the production of large numbers of high purity cortical NSCs, which are widely applicable for downstream research into developmental mechanisms, further differentiation into postmitotic cortical neurons, or other applications such as large-scale drug screening experiments.Peer reviewe

Population-scale proteome variation in human induced pluripotent stem cells

Human disease phenotypes are driven primarily by alterations in protein expression and/or function. To date, relatively little is known about the variability of the human proteome in populations and how this relates to variability in mRNA expression and to disease loci. Here, we present the first comprehensive proteomic analysis of human induced pluripotent stem cells (iPSC), a key cell type for disease modelling, analysing 202 iPSC lines derived from 151 donors, with integrated transcriptome and genomic sequence data from the same lines. We characterised the major genetic and non-genetic determinants of proteome variation across iPSC lines and assessed key regulatory mechanisms affecting variation in protein abundance. We identified 654 protein quantitative trait loci (pQTLs) in iPSCs, including disease-linked variants in protein-coding sequences and variants with trans regulatory effects. These include pQTL linked to GWAS variants that cannot be detected at the mRNA level, highlighting the utility of dissecting pQTL at peptide level resolution